Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,591,553 |
G→A |
47.9% |
P52P (CCG→CCA) |
hdeB → |
acid‑resistance protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,591,553 | 0 | G | A | 47.9%
| 3.6
/ 66.7
| 78 | P52P (CCG→CCA) | hdeB | acid‑resistance protein |
| Reads supporting (aligned to +/- strand): ref base G (18/22); new base A (25/12); total (43/35) |
| Fisher's exact test for biased strand distribution p-value = 6.62e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.24e-01 |
GCCAATGAATCCGCTAAAGATATGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGTATATAAAGGTGGC > minE/2591485‑2591598
|
gCCAATGAATCCTCTAAAGATATGACCTGCAAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCg < 1:13745/69‑1 (MQ=255)
gCCAATGAATCCGCTAAAGATATGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCg < 1:2229885/69‑1 (MQ=255)
gCCAATGAATCCGCTAAAGATATGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCg < 1:544902/69‑1 (MQ=255)
aTGAATCCGCTAAAGATATGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTg < 1:678556/69‑1 (MQ=255)
aTGAATCCGCTAAAGATATGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTg < 1:580987/69‑1 (MQ=255)
aTGAATCCGCTAAAGATATGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTg < 1:2548440/69‑1 (MQ=255)
aTGAATCCGCTAAAGATATGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTg < 1:3071837/69‑1 (MQ=255)
aTGAATCCGCTAAAGATATGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTg < 1:1451596/69‑1 (MQ=255)
gAATCCGCTAAAGATATGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCa > 1:1875512/1‑69 (MQ=255)
aaTCCGCTAAAGATATGACCTGCCAGGAATTTATTGATCTGAACCCAAAAGCAATGACCCCGGTTGCa > 1:401851/1‑68 (MQ=255)
cTAAAGATATGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGa < 1:1954301/69‑1 (MQ=255)
gATATGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGAtgctg < 1:3253997/69‑1 (MQ=255)
gATATGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGAtgctg < 1:1981225/69‑1 (MQ=255)
tatGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGAtgctgc > 1:2970085/1‑68 (MQ=255)
tatGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGAtgctgc > 1:1116392/1‑68 (MQ=255)
atGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCa < 1:1379866/54‑1 (MQ=255)
tGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGGTGCATGGTGGATGCTGCATg < 1:1522195/69‑1 (MQ=255)
cTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATgaaga > 1:3219275/1‑69 (MQ=255)
cTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATgaaga > 1:2337788/1‑69 (MQ=255)
cTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATgaaga > 1:2511546/1‑69 (MQ=255)
cAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGAtgctg < 1:2737703/57‑1 (MQ=255)
ggAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGt < 1:2514785/69‑1 (MQ=255)
aattaattGATCTGAATCCAAAAGCAATGACCCCGGTTGc < 1:2053347/40‑1 (MQ=255)
aaTTTATTGATCTGAATCCAAAAGCAATGACCCCTGTTGc < 1:936535/40‑1 (MQ=255)
aaTTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGc < 1:935726/40‑1 (MQ=255)
aaTTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGc < 1:1739159/40‑1 (MQ=255)
aaTTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGc < 1:1328851/40‑1 (MQ=255)
aTTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGtat > 1:309353/1‑68 (MQ=255)
aTTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGtat > 1:1128867/1‑68 (MQ=255)
aTTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGta > 1:3169053/1‑67 (MQ=255)
tATTGATCTGAATCCAAAAGCAATGCCCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGTATATaa > 1:998995/1‑69 (MQ=255)
tATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGtatata > 1:1042107/1‑68 (MQ=255)
tATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGTATATaa > 1:2192688/1‑69 (MQ=255)
tATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGTATATaa > 1:895921/1‑69 (MQ=255)
tATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGTATATaa > 1:3262756/1‑69 (MQ=255)
tATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGTATATaa > 1:1596527/1‑69 (MQ=255)
tATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGTATATaa > 1:205086/1‑69 (MQ=255)
tATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGTATATaa > 1:811720/1‑69 (MQ=255)
tATTGATCTGAATCCAAAAGCAATGACACCAGTTGCGTGGTGGATGCTGCATGAAGAAACAGTATATaa < 1:222171/69‑1 (MQ=255)
tATTGATCTGAATCCAAAAGCAATGACACCAGTTGCGTGGTGGATGCTGCATGAAGAAACAGTATATaa < 1:1769718/69‑1 (MQ=255)
tATTGATCTGAATCCAAAAGCAATGACACCAGTTGCGTGGTGGATGCTGCATGAAGAAACAGTATATaa < 1:1484541/69‑1 (MQ=255)
tATTGATCTGAATCCAAAAGCAATGACACCAGTTGCGTGGTGGATGCTGCATGAAGAAACAGTATATaa < 1:3344762/69‑1 (MQ=255)
tATTGATCTGAATCCAAAAGCAATGACACCAGTTGCGTGGTGGATGCTGCATGAAGAAACAGTATATaa < 1:3384322/69‑1 (MQ=255)
tATTGATCTGAATCCAAAAGCAATGACACCAGTTGCGTGGTGGATGCTGCATGAAGAAACAGTATATaa < 1:2817414/69‑1 (MQ=255)
tATTGATCTGAATCCAAAAGCAATGACACCAGTTGCGTGGTGGATGCTGCATGAAGAAACAGTATATaa < 1:1263590/69‑1 (MQ=255)
aTTGATCTGAATCCAAAAGCAATGACACCAGTTGCGTGGTGGATGCTGCATGAAGAAACAGTATATaa < 1:703579/68‑1 (MQ=255)
aTTGATCTGAATCCAAAAGCAATGACACCAGTTGCGTGGTGGATGCTGCATGAAGAAACAGTATATaa < 1:529735/68‑1 (MQ=255)
aTTGATCTGAATCCAAAAGCAATGACACCAGTTGCGTGGTGGATGCTGCATGAAGAAACAGTATATaa < 1:841863/68‑1 (MQ=255)
aTTGATCTGAATCCAAAAGCAATGACACCAGTTGCGTGGTGGATGCTGCATGAAGAAACAGTATATaa < 1:3187504/68‑1 (MQ=255)
ttGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGTATATaaa < 1:134944/68‑1 (MQ=255)
ttGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGTATATaaa < 1:3146391/68‑1 (MQ=255)
tCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGTATATAAAGGTGGc < 1:2739413/64‑1 (MQ=255)
tCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGTATATAAAGGTGGc < 1:2387040/64‑1 (MQ=255)
gaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:3144527/2‑41 (MQ=25)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:365905/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:1458018/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:53431/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:3292566/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:131199/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:3239106/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:2331697/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:1803127/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:1835813/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:188718/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:1897718/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:1936990/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:1666618/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:1615050/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:2241121/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:1431768/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:2368548/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:2696069/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:2854973/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:2928584/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:3091388/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:3107325/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCTGCATgaagaa > 1:3133940/1‑41 (MQ=37)
aaGCAATGACACCAGTTGCGTGGTGGATGCT‑CATgaagaa > 1:1535720/1‑40 (MQ=19)
gCAATGACACCAGTTGCGTGGTGGATGCTGCATGAAGAAACAGTATATaa < 1:1765783/50‑1 (MQ=255)
ccGGTTGCATGGTGGATGCTGCATGAAGAAACAGTATATAAAGGTGGc < 1:2055842/48‑1 (MQ=255)
ccGGTTGCATGGTGGATGCTGCATGAAGAAACAGTATATAAAGGTGGc < 1:3338598/48‑1 (MQ=255)
|
GCCAATGAATCCGCTAAAGATATGACCTGCCAGGAATTTATTGATCTGAATCCAAAAGCAATGACCCCGGTTGCATGGTGGATGCTGCATGAAGAAACAGTATATAAAGGTGGC > minE/2591485‑2591598
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
